![]() ![]() Instead I've been just opening every image in the directory one by one and applying the macro that I wrote, then saving the results manually. My approach has been to try and automate all the steps/ do batch processing but I have been having a hard time adapting what I have written to work based on instructions found online. Once the threshold is applied to the MIP, I convert it to binary and do particle analysis and save the results (summary table, results, image overlay. In my case 98% is what I am trying to achieve, eg thresholding all but the top 2% of the data. Currently, in FIJI if you go to image>adjust>threshold you can move the sliders such that a certain percentage of the image is thresholded and it will display that value for you in the open window. By relative value I mean that I would like to set the threshold so that the same % of the intensity histogram is included. This thresholding is one step causing a problem. Auto Uses the currently selected thresholding method to automatically set the threshold levels based on an analysis of the histogram of the current image or selection. ![]() Specifically, I'd like to open, smooth the image, do a Max intensity Z projection, then threshold the images to the same relative value. The problem is: when you run Image > Adjust > Threshold, the first thing that gets executed is an automatic threshold, and that is what gets recorded. I have a series of images all in the same folder and want to apply the same operations to them all and save the resultant excel files and images in an output folder. ![]() I know this has been posted elsewhere and that this is no means a difficult problem but I'm very new to writing macros in FIJI and am having a hard time even understanding the solutions described in various online resources. ![]()
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